Calling Somatic SNVs

4 important questions on Calling Somatic SNVs

G pop freqs

A list of common variants and their population frequencies to filter out mutations that are most likely germline variants

Reported issues with variant calling

  • Missing variants in BAM file
  • ClusterEvents filter out clinically relevant variants
  • Too many indels being called

Variant Effect Predictor (VEP)

Determines the effect of your variants on genes, transcripts, and protein sequence, as well as regulatory regions.
Gives location, consequence, known variants, affected genes etc.
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How to find driver genes?

  • Pathway analysis
  • Genes that are most often mutated in a certain cancer type

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